Neutrophilic inflammation in gallbladder carcinoma correlates with patient survival: A case-control study.

Gallbladder carcinoma is an uncommon malignancy with an overall 5-year survival of less than 5%. Gallbladder carcinoma has been strongly linked with cholelithiasis and chronic inflammation. Case reports and series have described cholecystitis with acute (neutrophilic) inflammation in association with gallbladder carcinoma, although a clear relationship to patient outcome has not been established.

species isolated from a chronic recurrent corneal ulcer.

Purpose: To report a case of recurrent corneal ulcer caused by an oropharyngeal cavity pathogen.

Observations: A patient presented with recurrent corneal ulcers with hypopyon. species was eventually isolated from the corneal ulcer on bacterial polymerase chain reaction (PCR) after many negative bacterial culture attempts.

Back Pain in a 23-Year-Old Male With X-Linked Chronic Granulomatous Disease.

Patients with chronic granulomatous disease are at increased risk for invasive aspergillosis. Cryptic species are being increasingly recognized as distinct causes of infection in this population. In this study, we describe the first case of vertebral osteomyelitis in a patient with X-linked chronic granulomatous disease.

Seasonal clustering of sinopulmonary mucormycosis in patients with hematologic malignancies at a large comprehensive cancer center.

Background: Invasive Mucorales infections (IMI) lead to significant morbidity and mortality in immunocompromised hosts. The role of season and climatic conditions in case clustering of IMI remain poorly understood.

Methods: Following detection of a cluster of sinopulmonary IMIs in patients with hematologic malignancies, we reviewed center-based medical records of all patients with IMIs and other invasive fungal infections (IFIs) between January of 2012 and August of 2015 to assess for case clustering in relation to seasonality.

Multifocal but non-disseminated phaeohyphomycosis in a healthy man via a unique mechanism: Ejection from motor vehicle accident into a vegetable field in Afghanistan resulting in multiple contaminated skin wounds.

A 20-year-old male presented with multiple subcutaneous nodules on the head, neck, chest and oral cavity. FNA and biopsy showed pigmented fungal hyphae diagnostic of multifocal phaeohyphomycosis, found to be Exophiala spinifera by molecular diagnostics. The presentation initially raised concern for disseminated disease and occult immunosuppression.

Can anaerobes be acid fast? A novel, clinically relevant acid fast anaerobe.

Introduction: Anaerobic acid fast bacilli (AFB) have not been previously reported in clinical microbiology. This is the second case report of a novel anaerobic AFB causing disease in humans.

Case Presentation: An anaerobic AFB was isolated from an abdominal wall abscess in a 64-year-old Caucasian diabetic male, who underwent distal pancreatectomy and splenectomy for resection of a pancreatic neuroendocrine tumour.

Incidental identification of Strongyloides stercoralis infection by broad-range 28S rDNA gene sequencing in a patient with a hematolymphoid malignancy.

Strongyloides stercoralis is an important human parasite, especially in rural areas and developing countries. Infected immunosuppressed patients are at risk for hyperinfection, with severe clinical consequences. Here we describe the incidental detection and diagnosis of an unexpected S.

Clinical Next Generation Sequencing Outperforms Standard Microbiological Culture for Characterizing Polymicrobial Samples.

Background: Humans suffer from infections caused by single species or more complex polymicrobial communities. Identification of infectious bacteria commonly employs microbiological culture, which depends upon the in vitro propagation and isolation of viable organisms. In contrast, detection of bacterial DNA using next generation sequencing (NGS) allows culture-independent microbial profiling, potentially providing important new insights into the microbiota in clinical specimens.

Rapid Detection of Vancomycin-Intermediate Staphylococcus aureus by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

Vancomycin is the standard of care for the treatment of invasive methicillin-resistantStaphylococcus aureus(MRSA) infections. Infections with vancomycin-nonsusceptible MRSA, including vancomycin-intermediateS. aureus(VISA) and heterogeneous VISA (hVISA), are clinically challenging and are associated with poor patient outcomes.

Bartonella quintana Aortitis in a Man with AIDS, Diagnosed by Needle Biopsy and 16S rRNA Gene Amplification.

A man with newly diagnosed AIDS presented with months of back pain and fever. Computed tomography (CT) results demonstrated aortitis with periaortic tissue thickening. DNA amplification of biopsy tissue revealed Bartonella quintana, and Bartonella serologies were subsequently noted to be positive.

Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology.

Nosocomial infections pose a significant threat to patient health; however, the gold standard laboratory method for determining bacterial relatedness (pulsed-field gel electrophoresis [PFGE]) remains essentially unchanged 20 years after its introduction. Here, we explored bacterial whole-genome sequencing (WGS) as an alternative approach for molecular strain typing. We compared WGS to PFGE for investigating presumptive outbreaks involving three important pathogens: vancomycin-resistant Enterococcus faecium (n=19), methicillin-resistant Staphylococcus aureus (n=17), and Acinetobacter baumannii (n=15).

Characterization of a multidrug-resistant, novel Bacteroides genomospecies.

Metronidazole- and carbapenem-resistant Bacteroides fragilis are rare in the United States. We isolated a multidrug-resistant anaerobe from the bloodstream and intraabdominal abscesses of a patient who had traveled to India. Whole-genome sequencing identified the organism as a novel Bacteroides genomospecies.

Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling.

High-throughput sequencing of the taxonomically informative 16S rRNA gene provides a powerful approach for exploring microbial diversity. Here we compare the performances of two common "benchtop" sequencing platforms, Illumina MiSeq and Ion Torrent Personal Genome Machine (PGM), for bacterial community profiling by 16S rRNA (V1-V2) amplicon sequencing. We benchmarked performance by using a 20-organism mock bacterial community and a collection of primary human specimens.

Whole genome sequencing indicates Corynebacterium jeikeium comprises 4 separate genomospecies and identifies a dominant genomospecies among clinical isolates.

Corynebacterium jeikeium is an opportunistic pathogen which has been noted for significant genomic diversity. The population structure within this species remains poorly understood. Here, we explore the relationships among 15 clinical isolates of C.

Whole-genome sequencing for high-resolution investigation of methicillin-resistant Staphylococcus aureus epidemiology and genome plasticity.

Methicillin-resistant Staphylococcus aureus (MRSA) infections pose a major challenge in health care, yet the limited heterogeneity within this group hinders molecular investigations of related outbreaks. Pulsed-field gel electrophoresis (PFGE) has been the gold standard approach but is impractical for many clinical laboratories and is often replaced with PCR-based methods. Regardless, both approaches can prove problematic for identifying subclonal outbreaks.

Coinfection of Fusobacterium nucleatum and Actinomyces israelii in mastoiditis diagnosed by next-generation DNA sequencing.

Some bacterial infections involve potentially complex mixtures of species that can now be distinguished using next-generation DNA sequencing. We present a case of mastoiditis where Gram stain, culture, and molecular diagnosis were nondiagnostic or discrepant. Next-generation sequencing implicated coinfection of Fusobacterium nucleatum and Actinomyces israelii, resolving these diagnostic discrepancies.

Molecular analysis of sarcoidosis lymph nodes for microorganisms: a case-control study with clinical correlates.

Introduction: Sarcoidosis is an incurable, chronic granulomatous disease primarily involving the lungs and lymph nodes of unknown aetiology, treated with non-specific anti-inflammatory/immunosuppressive drugs. Persistently symptomatic patients worsen with a disabling, potentially fatal clinical course. To determine a possible infectious cause, we correlated in a case-control study the clinical information with the presence of bacterial DNA in sarcoidosis mediastinal lymph nodes compared with control lymph nodes resected during cancer surgery.

Molecular diagnosis of Actinomadura madurae infection by 16S rRNA deep sequencing.

Next-generation DNA sequencing can be used to catalog individual organisms within complex, polymicrobial specimens. Here, we utilized deep sequencing of 16S rRNA to implicate Actinomadura madurae as the cause of mycetoma in a diabetic patient when culture and conventional molecular methods were overwhelmed by overgrowth of other organisms.

Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.

Classifying individual bacterial species comprising complex, polymicrobial patient specimens remains a challenge for culture-based and molecular microbiology techniques in common clinical use. We therefore adapted practices from metagenomics research to rapidly catalog the bacterial composition of clinical specimens directly from patients, without need for prior culture. We have combined a semiconductor deep sequencing protocol that produces reads spanning 16S ribosomal RNA gene variable regions 1 and 2 (∼360 bp) with a de-noising pipeline that significantly improves the fraction of error-free sequences.

Molecular diagnosis of subcutaneous Pythium insidiosum infection by use of PCR screening and DNA sequencing.

Pythium insidiosum is an emerging human pathogen classified among brown algae and diatoms that can cause significant morbidity and mortality in otherwise healthy individuals. Here we describe a pediatric patient with pythiosis acquired in the southern United States, diagnosed by molecular screening and DNA sequencing of internal transcribed spacer region 1.

Genome sequence of a novel species, Propionibacterium humerusii.

As part of a larger project to sequence multiple clinical isolates of Propionibacterium acnes, we have produced a draft genome sequence of a novel Propionibacterium species that is closely related to, yet distinct (by sequence) from P. acnes. We have tentatively named this new species Propionibacterium humerusii.

Molecular diagnosis of cystoisosporiasis using extended-range PCR screening.

The differential diagnosis of diarrhea in immunocompromised patients encompasses many intestinal parasites including the coccidian Cystoisospora belli. Gastrointestinal infection with C. belli leads to cystoisosporiasis with diarrhea and, depending on host immune status, can cause extraintestinal disease.

Ureaplasma urealyticum continuous ambulatory peritoneal dialysis-associated peritonitis diagnosed by 16S rRNA gene PCR.

In some patients with peritonitis complicating continuous ambulatory peritoneal dialysis (CAPD), a causative organism is never identified. We report a case of Ureaplasma urealyticum CAPD-associated peritonitis diagnosed by 16S rRNA gene PCR. Ureaplasma may be an underrecognized cause of peritonitis because it cannot be recovered using routine culture methods.

SeqSharp: A general approach for improving cycle-sequencing that facilitates a robust one-step combined amplification and sequencing method.

Sequencing a specific DNA element within a genome or a complex mixture of DNA by the Sanger sequencing method generally involves PCR-mediated amplification of target DNA with forward and reverse primers, followed by a sequencing reaction directed from a single primer. To minimize the contribution of fluorescent signal due to the extension products originating from primers carried over from the amplification step, an intermediate step is routinely incorporated to remove the excess primers before proceeding to the sequencing reaction. We have developed a method called SeqSharp that removes noise in the sequencing data by enzymatically removing chain termination products originating from one or both of the amplification primers.